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General Barcode Information from Alignments

This report aggregates the barcode-specific information from the alignments that were created using harpy align. Detailed information for any one sample can be found in that sample’s individual report. The table below is an aggregation of data for each sample based on their *.bxstats.gz file.

• avg refers to the average (arithmetic mean)
• SEM refers to the Standard Error of the mean
• molecules are the unique DNA molecules as inferred from linked-read barcodes
• barcodes are the linked-read barcodes associated with DNA sequences and are synonymous with bx
• valid refers to a proper haplotag barcode (e.g. A01C34B92D51)
• invalid refers to an invalidated haplotag barcode, where there is a 00 in any of the ACBD positions (e.g. A21C00B32D57)
• NX are the N-statistics (explained in more detail below)

Per-Sample Information

NX desc

NX Information

The NX metric (e.g. N50) is the length of the shortest molecule in the group of longest molecules that together represent at least X% of the total molecules by length. For example, N50 would be the shortest molecule in the group of longest molecules that together represent 50% of the total molecules by length. Below is the distribution of three common NX metrics (N50, N75, N90) across all samples.

NX plots

dist description

Distribution of alignments with valid barcodes

Below is a distribution of what percent of total alignments each sample had valid haplotag barcodes (AXXCXXBXXDXX where XX is not 00).

distribution plot

Per-sample desc

Per-Sample Metrics

Below is a series of plots that shows metrics per-sample.

percent valid

molecules per contig

reads per molecule